Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate N515DRAFT_3308 N515DRAFT_3308 acetylornithine/N-succinyldiaminopimelate aminotransferase
Query= SwissProt::Q5JEW1 (445 letters) >FitnessBrowser__Dyella79:N515DRAFT_3308 Length = 411 Score = 177 bits (449), Expect = 6e-49 Identities = 126/413 (30%), Positives = 203/413 (49%), Gaps = 45/413 (10%) Query: 38 IVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYE 97 +V++ G+G RV+D +G + D +G+ V +GH P +V+A+ QA K H S F+ E Sbjct: 27 VVLDHGKGARVWDTEGRDYVDLGAGIAVNALGHQDPDLVDALVTQARKLWHSSNV-FYTE 85 Query: 98 NAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQ-------FLAFYHA 150 + LAE+L++ A G ER V NSG EANEAA+KLV+ K L F + Sbjct: 86 PPLHLAEELVQ-ASGFAER-VFLCNSGTEANEAAIKLVRKWAASKGRAPEQRVILTFRGS 143 Query: 151 FHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDF 210 FHGRT A ++ TA Q++ + P P +R Y + +++ F Sbjct: 144 FHGRTLAAVTATAQPKYQEN----------YEPLPGGFR-------YLDFNDVAGLEAAF 186 Query: 211 IEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIG 270 + ++ A+ EP+QGEGG + F + ++ D + LL DE+Q G+G Sbjct: 187 AQG---------DVAAVMLEPVQGEGGVLPASPAFIRRARELCDTHEALLVLDEIQCGMG 237 Query: 271 RTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADIT-FDKPGRHATTFGGNPVAIA 329 RTG +A GV PD++ KA+G G P+ ++ + + G H TTFGGNP+A A Sbjct: 238 RTGTLFAHAQDGVTPDIVTLAKALGCGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAA 297 Query: 330 -AGIEVVEIVK-ELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETK 387 A + + ++ EL+ +V + L L + ++ + RG GL + Sbjct: 298 VARVALRKLASAELMANVAKQAQALRDGLAAIDGELKLFAEVRGRGLMLGAVLA------ 351 Query: 388 EKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEAL 440 E Y ++ +A GL++L G + +RF+PPL +T ++ + AL Sbjct: 352 EAYKGRAGEVLDHAAAHGLLVLQAGPDVLRFVPPLNITDADLAEGLARLRAAL 404 Lambda K H 0.320 0.141 0.418 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 420 Number of extensions: 30 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 445 Length of database: 411 Length adjustment: 32 Effective length of query: 413 Effective length of database: 379 Effective search space: 156527 Effective search space used: 156527 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory